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genomoncology/biomcp

Free

生物医学研究服务器，提供对 PubMed、ClinicalTrials.gov 和 MyVariant.info 的访问。

FreeFree tier
Type
Open Source
Company
genomoncology
Visit Website GitHub (40 stars)

About genomoncology/biomcp

BioMCP is a single-binary CLI tool and Model Context Protocol (MCP) server that provides unified access to approximately 30 trusted biomedical databases including PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, and more. Using a single command grammar, users can search literature, pivot between genes, variants, drugs, diseases, and pathways without rebuilding workflows. It supports local study analysis with terminal and SVG/PNG charts for cBioPortal-style datasets, enrichment via g:Profiler, batch queries, and integration with AI agents such as Claude Code, Codex, and Claude Desktop. The tool is free, open-source, and designed for researchers, clinicians, and agents needing efficient, evidence-oriented biomedical data retrieval and analysis.

Key Features

Unified access to ~30 trusted biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, etc.) via a single command grammar
Search literature across PubTator3, Europe PMC, and Semantic Scholar with deduplication of identifiers
Pivot between genes, variants, drugs, diseases, pathways, proteins, and articles without rebuilding filters
Pre-built skill playbooks for common workflows (biomcp skill list)
Local study analysis with commands for query, cohort, survival, compare, and co-occurrence workflows, including terminal, SVG, and PNG charts
Paper trail commands for citations, references, recommendations, and entity extraction
Enrichment via g:Profiler and batch queries (up to 10 focused calls in one command)
MCP server integration with AI agents (Claude Code, Codex, Claude Desktop)

Pros & Cons

Pros
  • Unifies access to ~30 major biomedical sources in a single command-line interface
  • Free and open-source with no licensing costs
  • Supports local, offline analysis of study data with built-in chart generation
  • Compatible with popular AI coding assistants via the Model Context Protocol
  • Pivot queries across multiple biomedical entities without rebuilding filters

Best For

Biomedical literature search and evidence mapping across multiple public databasesClinical trial and variant information retrieval for cancer research (e.g., BRAF in melanoma)Local analysis of cBioPortal-style study datasets with survival and co-occurrence chartsAutomated data enrichment and batch queries for large-scale biomedical projectsIntegration of biomedical evidence into AI agent workflows via the MCP standard

FAQ

What is BioMCP?
BioMCP is a CLI binary and MCP server that provides a unified command grammar to query ~30 trusted biomedical sources (PubMed, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, etc.) and perform local study analysis.
How do I install BioMCP?
You can install via binary with curl -fsSL https://biomcp.org/install.sh | bash, via pip/uv tool: uv tool install biomcp-cli or pip install biomcp-cli, or run via Docker (Dockerfile provided in the repository).
What sources does BioMCP support?
BioMCP reaches ~30 sources including PubMed, PubTator3, Europe PMC, Semantic Scholar, ClinVar, ClinicalTrials.gov, OncoKB, Reactome, g:Profiler, and more.
Can BioMCP be used with AI agents?
Yes, BioMCP is an MCP server, so it integrates with AI agents like Claude Code, Codex, and Claude Desktop using the same tools available via command line.